Strain identifier

BacDive ID: 140372

Type strain: Yes

Species: Actinomyces gaoshouyii

Strain Designation: pika_113

Strain history: <- X. Meng, Chinese Center for Disease Control and Prevention, Beijing, China; pika_113

NCBI tax ID(s): 1960083 (species)

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General

@ref: 42979

BacDive-ID: 140372

DSM-Number: 104049

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped, colony-forming

description: Actinomyces gaoshouyii pika_113 is a facultative anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from intestinal contents of plateau pika .

NCBI tax id

  • NCBI tax id: 1960083
  • Matching level: species

strain history

  • @ref: 42979
  • history: <- X. Meng, Chinese Center for Disease Control and Prevention, Beijing, China; pika_113

doi: 10.13145/bacdive140372.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Actinomycetales
  • family: Actinomycetaceae
  • genus: Actinomyces
  • species: Actinomyces gaoshouyii
  • full scientific name: Actinomyces gaoshouyii Meng et al. 2017

@ref: 42979

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinomycetaceae

genus: Actinomyces

species: Actinomyces gaoshouyii

full scientific name: Actinomyces gaoshouyii Meng et al. 2017

strain designation: pika_113

type strain: yes

Morphology

cell morphology

  • @ref: 43895
  • gram stain: positive
  • cell length: 1.1-1.6 µm
  • cell width: 0.4-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43895
  • colony size: <1 mm
  • colony color: greyish white
  • colony shape: circular
  • incubation period: 1 day
  • medium used: Columbia blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43895Brain heart infusionyes
43895Columbia blood agaryes
42979COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
42979BBL ACTINOMYCES BROTH (DSMZ Medium 1029)yeshttps://mediadive.dsmz.de/medium/1029Name: BBL ACTINOMYCES BROTH (DSMZ Medium 1029) Composition: Infusion Broth 1.425 g/l Potassium Phosphate 0.855 g/l Dextrose 0.285 g/l Yeast extract 0.285 g/l Pancreatic digest of casein 0.228 g/l L-Cysteine HCl 0.057 g/l Starch 0.057 g/l Ammonium Sulfate 0.057 g/l Magnesium sulfate 0.0114 g/l Calcium Chloride 0.00057 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43895positiveoptimum30mesophilic
42979positivegrowth37mesophilic

culture pH

  • @ref: 43895
  • ability: positive
  • type: optimum
  • pH: 6.0-7.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43895
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 43895
  • spore formation: no

halophily

  • @ref: 43895
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43895168082-dehydro-D-gluconate-builds acid from
4389515963ribitol-builds acid from
4389517108D-arabinose-builds acid from
4389528847D-fucose-builds acid from
4389562318D-lyxose-builds acid from
4389517924D-sorbitol-builds acid from
4389516443D-tagatose-builds acid from
4389565327D-xylose-builds acid from
4389516813galactitol-builds acid from
4389517113erythritol-builds acid from
4389528087glycogen-builds acid from
4389530849L-arabinose-builds acid from
4389518403L-arabitol-builds acid from
4389518287L-fucose-builds acid from
4389562345L-rhamnose-builds acid from
4389517266L-sorbose-builds acid from
4389517716lactose-builds acid from
4389543943methyl alpha-D-mannoside-builds acid from
4389574863methyl beta-D-xylopyranoside-builds acid from
43895506227N-acetylglucosamine-builds acid from
4389532032potassium gluconate-builds acid from
4389517151xylitol-builds acid from
438955291gelatin-hydrolysis
43895581435-dehydro-D-gluconate+builds acid from
4389527613amygdalin+builds acid from
4389518305arbutin+builds acid from
4389517057cellobiose+builds acid from
4389518333D-arabitol+builds acid from
4389515824D-fructose+builds acid from
4389512936D-galactose+builds acid from
4389517634D-glucose+builds acid from
4389516899D-mannitol+builds acid from
4389516024D-mannose+builds acid from
4389516988D-ribose+builds acid from
438954853esculin+builds acid from
4389528066gentiobiose+builds acid from
4389517754glycerol+builds acid from
4389517268myo-inositol+builds acid from
4389515443inulin+builds acid from
4389517306maltose+builds acid from
4389528053melibiose+builds acid from
43895320061methyl alpha-D-glucopyranoside+builds acid from
4389516634raffinose+builds acid from
4389517814salicin+builds acid from
4389528017starch+builds acid from
4389517992sucrose+builds acid from
4389527082trehalose+builds acid from
4389532528turanose+builds acid from
43895606565hippurate+hydrolysis
4389517632nitrate+reduction

enzymes

@refvalueactivityec
43895catalase-1.11.1.6
43895alkaline phosphatase+3.1.3.1
43895esterase (C 4)+
43895leucine arylamidase+3.4.11.1
43895valine arylamidase+
43895cystine arylamidase+3.4.11.3
43895acid phosphatase+3.1.3.2
43895naphthol-AS-BI-phosphohydrolase+
43895alpha-galactosidase+3.2.1.22
43895beta-galactosidase+3.2.1.23
43895alpha-glucosidase+3.2.1.20
43895beta-glucosidase+3.2.1.21
43895pyrazinamidase+3.5.1.B15
43895esterase Lipase (C 8)-
43895lipase (C 14)-
43895trypsin-3.4.21.4
43895alpha-chymotrypsin-3.4.21.1
43895beta-glucuronidase-3.2.1.31
43895N-acetyl-beta-glucosaminidase-3.2.1.52
43895alpha-mannosidase-3.2.1.24
43895alpha-fucosidase-3.2.1.51
43895pyrrolidonyl arylamidase-3.4.19.3
43895arginine dihydrolase-3.5.3.6
43895pyroglutamic acid arylamidase-
43895glycyl tryptophan arylamidase-
43895urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture duration
42979intestinal contents of plateau pika (Ochotona curzoniae)Ochotona curzoniaeTibet-Qinghai PlateauChinaCHNAsia
43895intestinal contents of plateau pika (Ochotona curzoniae), Tibet-Qinghai Plateau, ChinaTibet-Qinghai PlateauChinaCHNAsiaColumbia-5% sheep blood agar1 day

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Caecal content
#Host#Mammals
#Host Body Product#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_4257.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_124;96_1160;97_2586;98_3206;99_4257&stattab=map
  • Last taxonomy: Actinomyces
  • 16S sequence: KY611802
  • Sequence Identity:
  • Total samples: 5471
  • soil counts: 33
  • aquatic counts: 84
  • animal counts: 5344
  • plant counts: 10

Safety information

risk assessment

  • @ref: 42979
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42979
  • description: Actinomyces gaoshouyii 16S ribosomal RNA gene, partial sequence
  • accession: KY611802
  • length: 1466
  • database: ena
  • NCBI tax ID: 1960083

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinomyces gaoshouyii CGMCC 4.7372GCA_014646495scaffoldncbi1960083
66792Actinomyces gaoshouyii pika_113GCA_002072175scaffoldncbi1960083
66792Actinomyces gaoshouyii strain CGMCC 4.73721960083.5wgspatric1960083

GC content

@refGC-contentmethod
4389571genome sequence analysis
4297971sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.263yes
gram-positiveyes96.348no
anaerobicno91.8yes
aerobicno95.778yes
halophileno90.229yes
spore-formingno95.934no
thermophileno84.03no
glucose-utilyes89.568no
motileno92.421no
glucose-fermentyes86.14no

External links

@ref: 42979

culture collection no.: DSM 104049, CGMCC 4.7372

straininfo link

  • @ref: 96670
  • straininfo: 399218

literature

  • topic: Phylogeny
  • Pubmed-ID: 28857023
  • title: Actinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae).
  • authors: Meng X, Wang Y, Lu S, Lai XH, Jin D, Yang J, Xu J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002119
  • year: 2017
  • mesh: Actinomyces/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, DNA, Bacterial/genetics, Intestines/*microbiology, Lagomorpha/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
42979Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104049Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104049)
43895Xiangli Meng, Yiting Wang, Shan Lu, Xin-He Lai, Dong Jin, Jing Yang, Jianguo XuActinomyces gaoshouyii sp. nov., isolated from plateau pika (Ochotona curzoniae)10.1099/ijsem.0.002119IJSEM 67: 3363-3368 201728857023
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96670Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID399218.1